Status
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Gene information
General information
TC006335 Gene

The sequence from the iB fragment is matched against the genes from the official gene set. The matche(s) is/are visualizied in a genome browser.

NC_007423.3: 7354376..7356045
Sequence information
Transcripts / Proteins (1) Get mRNA sequence
Get CDS sequence
Get protein sequence
Ortholog information (from OrthoDB)

The information about the homolog genes in Drosophila is provided by OrthoDB http://www.orthodb.org/. The homologs are sorted according to their similarity score. For an orthology statement additional analysis are required.
The data basis for the orthologs is OrthoDB v9 containing OGS3 for Tribolium castaneum and 2015_04 (r6.07) for Drosophila melanogaster.

Closest fly homologs
      		TC006335
      Gene ontology

      GO terms for Tribolium

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      There are no GO terms for Tribolium at the moment. You can help the community by providing some GO terms for this gene.


      GO terms for the homologous Drosophila genes

      Assign a GO term to this Tribolium gene by filling in the fields. Repeat to add several GO terms. Search AmiGO for the correct GO ID. Use only the most specific term - use "graph views" to browse related terms ("child terms" are more specific; the more general "parent" terms will be automatically linked). Only information based on Tribolium data should be entered - do not define terms just based on Drosophila knowledge. We will review this information and submit the annotation to the Gene Ontology consortium.


      Gene
      {{ goGene }}
      The Tribolium gene the GO term is assigned to.
      GO ID *
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      The ID of the GO term you assign to the gene. Please enter only the ID of the GO term with proceeding 'GO:'. This information is mandatory.
      Evidence
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      The evidence code describes with which method the function or location, expressed by the GO term, was show for this gene. Please refer to this page for a definition of the evidence code and a decision tree.
      Reference *
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      The reference where the function or location is described for the gene. Please enter a PubMed ID. This information is mandatory.
      Quotation
      If you paste here the relevant section of the reference it is for us a great help to review your annotation. The quotation may be also be displayed to the users of iBeetle-Base.
      Name
      You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
      Email
      We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
      Publish name
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      * : mandatory fields
      For help on how to submit larger datasets or non experimental data please contact us.
      iBeetle screen iB_04116

      Attention! iBeetle is a first pass screen. Hence, the documented phenotypes need to be confirmed by independent experiments using non-overlapping dsRNA fragments! Phenotypes with a penetrance > 50% are frequently reproduced. See Schmitt-Engel et al. 2015 for details on reproducibility.

      iB sequence
      Phenotype after pupal injection
      Usually 10 injected animals

      Pupal injection procedure

      Day 0: 10 female pupae of the pBA19 strain (muscle enhancer trap line) were injected with dsRNA.

      3 days post injection (dpi): Hatch control: Pupal and adult lethality as well as metamorphosis defects (molting, eclosion) were documented. For mating, 4 males of the black strain were added.

      9 dpi: First egg-lay was collected and incubated for cuticle analysis. Adult lethality and egg production (reduced/ no egg-lay) was documented.

      11 dpi: Second egg-lay was collected and incubated for embryonic muscle analysis. Adult lethality and egg production (reduced/ no egg-lay) were documented.

      Note: The adult morphology was not analyzed systematically at 3/9/11 dpi. Only obvious phenotypes, visible without magnification, have been annotated.

      13 dpi: Egg productivity and Ovary analysis
      The percentage of hatched larvae was documented and not hatched larvae/ eggs were embedded for cuticle analysis (15 dpi). In case of a reduction of egg production, 4 injected females were dissected to analyze the gross morphology of the ovaries.

      14 dpi: Analysis of embryonic musculature and early embryonic development
      Offspring of the injected females (hatched and not hatched larvae/ eggs) were analysed for embryonic lethality and muscle defects.

      15 dpi: Analysis of larval instar 1 cuticle
      Offspring of injected females were analysed and cuticle phenotypes were annotated.

      22 dpi: Stink gland analysis
      Documentation of defects in abdominal and thoracic stink glands (colour, size, content) of the injected femals.

      Terms used in the pupal injection procedure

      larval pantagmatic defects
      At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
      empty eggs
      Just empty shells are visible, no cuticle has been developed.
      strong defects
      L1 cuticle larvae which show severe defects. These strong defects are subdivided into three categories
      strongly fragmented (cuticle crumbs)
      No segments or appendages are identifiable, only residues of cuticle and bristles can be identified.
      cuticle remnants (with unidentifiable segments)
      Segments or parts of appendages are recognizable, but identity is not clear.
      cuticle remnants (with some identifiable segments)
      At least one segment or appendage is clearly regonizable.
      number of eggs on slide
      affected embryos usually (not always) do not hatch. Only the not hatched were used for cuticle analysis.
      For the embryonic muscle analysis the hatched as well as the not hatched were analysed.
      total number of affected eggs/embryos/larvae
      Summary of all different phenotypes/ phenotypic series which were annotated.
      inside-out
      The L1 larva shows a partial or complete inversion., e.g. bristles, appendages or parts of the abdominal segments are inverted into the interior of the cuticle.
      starved
      Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
      eclosion not fulfilled
      The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
      Please see the help page for more information
      Metamorphosis and survival

      Lethality 11 days after pupal injection: 0.0% (includes death as pupa, adult)

      Analysis of larval stage 1 cuticle
      number of eggs/embryos/larvae on slide: < 50
       procephalic appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      procephalic head partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%
      affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 80%
      Phenotype after larval injection
      Usually 10 injected animals

      Larval injection procedure

      Day 0: 10 female L5-6 larvae of the D17Xhom strain (females express RFP in the eyes and in the CNS; pupae express GFP in the thorax) were injected with dsRNA.

      11 days post injection (dpi): Pupal morphology Documentation of larval/ pupal death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of pupal head and appendages, pupal thorax, pupal thoracic musculature, pupal legs, pupal wings, pupal abdomen and pupal genital lobes.

      16 dpi: Adult morphology Documentation of larval/ pupal and adult death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of adult head and appendages, adult thorax, adult elytra and hindwings, adult legs and cuticle properties. For mating 4 males of the black strain were added.

      19 dpi: Sieving and egg-lay Documentation of adult lethality and enduring metamorphosis defects.

      22 dpi: Ovary analysis (Fertility) In case of a reduction of egg production 4 females were dissected and the gross morphology of the ovaries were analysed.

      41 dpi: Fertility and stink gland analysis Documentation of defects in abdominal and thoracic stink glands development (colour, size, content) of the injected females. Check for fertility of injected larvae (no or decreased offspring).

      Terms used in the larval injection procedure

      pupal/ adult pantagmatic defects
      At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
      pupal molt not fulfilled
      The hatching from the larva to the pupa is interrupted. Either it dies as prepupa or the phenotype shows larval as well as pupal features.
      eclosion not fulfilled
      The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
      starved
      Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
      Metamorphosis and survival

      Lethalities 11 days after larval injection: 20.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC006335 RA
        MIESPSCHA EALQHEIHK SVSSLHQRL VAPPTDLTQ 
KIQQLIHGN TILTYYLRM SWLRKLSFL NELIKRIKS 
LDTMRLVID TLQPLLGKL TSYCKSTTA TPMNFDKVL 
NDHDRMFSG DILEENIAL DLAWFESIE DQEQVAYLI 
AFIRLSGHA LIRIFIANL QSALVERLK VQALQANHI 
DEKEEKKNS SESHYKHDL DDPKHQKCV QLQKKWEKT 
IGEYRKKVL GKKKEKAST KSKDKKSKN KKTKKAKKK 
NKKKRKGGK DEPLDWIQI MPIMIVKKI FNHLDKKSL 
NRAKKVNTY WKWAIGELL KDRKARKSL NKSDKKLRK 
ASGSECFFP ESEFLEGKA RVSHTERRL QKLQMRGAI 
LEELRQNSR VAQNTNALI TEAMKLAPY VSDLTMYPR 
VERKNGAIF KRPEFLVKD LGIICVEGD DLSESEEDT 
GGQGTRFSS SVASSGSDR F
      CDS sequence
      • >TC006335 RA
        atgatcgaa tcaccttct tgccacgct gaagctttg 
caacatgaa atccacaaa tccgttagt tccctccac 
caacgcctg gtcgcacca cccactgac ctgacccaa 
aaaatccaa caactgatt cacggaaac actattcta 
acgtactac ttgcgcatg tcatggctg cgaaaatta 
tcatttttg aacgaatta atcaaaaga atcaaaagt 
ctggacacc atgagacta gtgatagat acactgcag 
ccacttttg ggaaaatta acgtcttac tgcaagtcg 
accactgca actccgatg aattttgat aaggttttg 
aatgaccat gaccgcatg ttcagtggc gatattttg 
gaggaaaat atcgccttg gatttggct tggtttgag 
tcgattgaa gaccaggaa caagttgcg tatcttatt 
gcctttatc agactttcg ggtcatgcg ttaatccgc 
attttcatt gcaaatttg caatcagcg cttgtggaa 
cgcttgaaa gtccaagcg cttcaagcc aaccacatt 
gacgaaaaa gaggagaag aaaaacagc tctgaaagc 
cactacaag catgatttg gacgacccg aagcaccaa 
aagtgtgtc caattgcag aaaaagtgg gagaaaacc 
atcggggaa taccggaag aaagtgctc ggtaaaaaa 
aaagaaaaa gcttcgacg aaatcaaaa gacaaaaag 
agtaaaaac aaaaaaact aagaaggcg aagaaaaaa 
aataaaaag aagagaaaa ggtggtaaa gatgagccc 
cttgattgg atccagata atgccaatc atgatcgtg 
aaaaaaatc ttcaaccac ttggacaaa aaatcgcta 
aaccgagcc aagaaagtc aacacttac tggaaatgg 
gcgattggt gagttgctc aaagaccgc aaagctcgc 
aaatcgttg aacaaaagc gacaaaaag ctccggaaa 
gcctccgga agtgagtgt ttttttccg gagagtgag 
tttttggag ggcaaagca cgcgtgagt cacactgaa 
cgaaggctc cagaagctg caaatgcga ggtgcgatt 
ttggaggag ttgcgacaa aattcccgt gtggctcaa 
aacacgaat gctcttatc accgaagcg atgaaattg 
gcgccgtat gtgagcgat ttgacgatg tatccgaga 
gttgagcgg aaaaatggg gcgattttt aagaggccg 
gagtttctt gtcaaagat ttggggata atttgcgtg 
gagggggat gatttgtcc gagtcggag gaggataca 
ggggggcag ggaacgcgg ttttcgtcg tcggttgcg 
tcaagtggc agcgacagg ttttga
      mRNA sequence
      • >TC006335 RA
        ttcaataaa aataatcaa gtaataaga atccagtcg 
ccttgaact tgtcaaatc ccgcgtcat gatcgaatc 
accttcttg ccacgctga agctttgca acatgaaat 
ccacaaatc cgttagttc cctccacca acgcctggt 
cgcaccacc cactgacct gacccaaaa aatccaaca 
actgattca cggaaacac tattctaac gtactactt 
gcgcatgtc atggctgcg aaaattatc atttttgaa 
cgaattaat caaaagaat caaaagtct ggacaccat 
gagactagt gatagatac actgcagcc acttttggg 
aaaattaac gtcttactg caagtcgac cactgcaac 
tccgatgaa ttttgataa ggttttgaa tgaccatga 
ccgcatgtt cagtggcga tattttgga ggaaaatat 
cgccttgga tttggcttg gtttgagtc gattgaaga 
ccaggaaca agttgcgta tcttattgc ctttatcag 
actttcggg tcatgcgtt aatccgcat tttcattgc 
aaatttgca atcagcgct tgtggaacg cttgaaagt 
ccaagcgct tcaagccaa ccacattga cgaaaaaga 
ggagaagaa aaacagctc tgaaagcca ctacaagca 
tgatttgga cgacccgaa gcaccaaaa gtgtgtcca 
attgcagaa aaagtggga gaaaaccat cggggaata 
ccggaagaa agtgctcgg taaaaaaaa agaaaaagc 
ttcgacgaa atcaaaaga caaaaagag taaaaacaa 
aaaaactaa gaaggcgaa gaaaaaaaa taaaaagaa 
gagaaaagg tggtaaaga tgagcccct tgattggat 
ccagataat gccaatcat gatcgtgaa aaaaatctt 
caaccactt ggacaaaaa atcgctaaa ccgagccaa 
gaaagtcaa cacttactg gaaatgggc gattggtga 
gttgctcaa agaccgcaa agctcgcaa atcgttgaa 
caaaagcga caaaaagct ccggaaagc ctccggaag 
tgagtgttt ttttccgga gagtgagtt tttggaggg 
caaagcacg cgtgagtca cactgaacg aaggctcca 
gaagctgca aatgcgagg tgcgatttt ggaggagtt 
gcgacaaaa ttcccgtgt ggctcaaaa cacgaatgc 
tcttatcac cgaagcgat gaaattggc gccgtatgt 
gagcgattt gacgatgta tccgagagt tgagcggaa 
aaatggggc gatttttaa gaggccgga gtttcttgt 
caaagattt ggggataat ttgcgtgga gggggatga 
tttgtccga gtcggagga ggatacagg ggggcaggg 
aacgcggtt ttcgtcgtc ggttgcgtc aagtggcag 
cgacaggtt ttgagggat tataaatta ttatttggg 
agcggtcac aaattaatt aaaacgatt tagttgaa

      If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
      Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

      The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY